May 6, 2022

Happy Friday! Today’s microbiome digest is a grab bag of articles on topics such as antibiotic cycling and bacterial contamination in surgery, phage isolated from diseased seafood, and microbial communities in snuff. I was particularly interested to see the article focused on degradation genes found in steel industrial soil communities. Finally, I enjoyed checking out two preprints on oral microbiota in Agta, a group of hunter-gatherers from the Philippines.

General microbiome

Preprint: The making of the oral microbiome in Agta hunter-gatherers – Dobon et al. – bioRxiv

Preprint: Microbial population dynamics decouple nutrient affinity from environmental concentration – Fink et al. – bioRxiv

Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand – Huang et al. – PLOS Pathogens

Preprint: Hunter-gatherer oral microbiomes are shaped by contact network structure – Muscitto et al. – bioRxiv

Which vaccine attributes foster vaccine uptake? A cross-country conjoint experiment – Stöckli et al. – PLOS ONE

Associations between microbial communities and key chemical constituents in U.S. domestic moist snuff – Tyxobert et al. – PLOS ONE

Multi-site human microbiome

Mycobacterium tuberculosis infection, immune activation, and risk of HIV acquisition – Bender Ignacio et al. – PLOS ONE

The effects of antibiotic cycling and mixing on acquisition of antibiotic resistant bacteria in the ICU: A post-hoc individual patient analysis of a prospective cluster-randomized crossover study – van Duijin et al. – PLOS ONE

Human gut microbiome

Efficacy of laparotomy sponges to reduce bacterial contamination using an in vitro gastrointestinal surgery model – Bezhentseva et al. – PLOS ONE

Animal experiments

Virulence and antimicrobial resistance gene profiles of Staphylococcus aureus associated with clinical mastitis in cattle – Neelam et al. – PLOS ONE

Preexisting Trichinella spiralis infection attenuates the severity of Pseudomonas aeruginosa-induced pneumonia – Rong Long et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil – Sandhu et al. – PLOS ONE

Water and extremophile microbiome

Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl – Rivera-Araya et al. – PLOS ONE

Food microbiology

Sole and combined effect of foliar zinc and arbuscular mycorrhizae inoculation on basmati rice growth, productivity and grains nutrient – Mehmood et al. – PLOS ONE

Characterization and complete genome sequence analysis of a newly isolated phage against Vibrio parahaemolyticus from sick shrimp in Qingdao, China – Tian et al. – PLOS ONE


Financial incentives to increase stool collection rates for microbiome studies in adult bone marrow transplant patients – Thompson et al. – PLOS ONE

April 8, 2022

Good morning! Today’s microbiome digest is brought to you by mild insomnia induced by a mid-afternoon coffee. It includes two food related studies, one on pathogenic E. coli found in ready-to-eat foods and the other focused on a antifungal lipopeptide produced by B. velezensis isolated from honey, and an an article focused on a new approach for processing frozen lung and lavage samples for use in microbiome studies. Also included are several articles focused on the gut microbiome, and several preprints focused on soil microbiome studies. Finally, I want to highlight a piece that details the positive outcomes associated with the National Summer Undergraduate Research Project (NSURP). Registration for this year’s program is still open until April 15th, and the organizers are looking for both mentors, mentees, and donors!

Pregnancy and early life

Group B Streptococcus colonization at delivery is associated with maternal peripartum infection – Brigtsen et al. – PLOS ONE

Human gut microbiome

Mycobacterium avium subsp. paratuberculosis and microbiome profile of patients in a referral gastrointestinal diseases centre in the Sudan – Elmagzoub et al. – PLOS ONE

Animal experiments

Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life – Brand et al. – PLOS ONE

Sex differences in the fecal microbiome and hippocampal glial morphology following diet and antibiotic treatment – Saxena et al. – PLOS ONE

Animal microbiome

Preprint: Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate – Wasimuddin et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago – Schoenborn et al. bioRxiv

Preprint: The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types – Vitamaki et al. – bioRxiv

Preprint: Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil – Wilhelm et al. – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Preprint: Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments – Kohtz et al. – bioRxiv

Food microbiology

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health – Beshiru et al. – PLOS ONE

Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey – Ziong et al. – PLOS ONE


An optimized approach for processing of frozen lung and lavage samples for microbiome studies – Wiscovitch-Russo et al. – PLOS ONE

Science, publishing, and career

***National Summer Undergraduate Research Project (NSURP): A Virtual Research Experience to Deliver REAL (Retention, Equity, Access, and Life-Changing) Outcomes for Underrepresented Minorities in STEM – Johnson & Knox – JMBE

January 7, 2022

Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes

January 4, 2022

Happy new year! Today’s digest is jam packed with articles published over the Christmas period. This includes the Skin Microbial Genome Collection (SMGC), a fascinating study linking the gut virome to rotavirus vaccine response, multiple cancer-microbiome papers and a catalogue of the human gut archaeome

General microbiome

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes – Bossche et al. Microbiome

Directional Gaussian Mixture Models of the Gut Microbiome Elucidate Microbial Spatial Structure – Pasarkar et al. mSystems

Human gut microbiome

Human gut-microbiome-derived propionate coordinates proteasomal degradation via HECTD2 upregulation to target EHMT2 in colorectal cancer – Ryu et al. ISME

Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network – Goffau et al. Nature Microbiology.

Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance – Bell et al. Cancer Cell. 

Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease – Walker et al. Genome Medicine

Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants – Kim et al. Cell Host & Microbe

Maternal gut bacteria drive intestinal inflammation in offspring with neurodevelopmental disorders by altering the chromatin landscape of CD4+ T cells – Kim et al. Immunity

Lactobacillus gallinarum modulates the gut microbiota and produces anti-cancer metabolites to protect against colorectal tumourigenesis – Sugimura et al. Gut

A catalogue of 1,167 genomes from the human gut archaeome – Chibani et al. Nature Microbiology

Variation and transmission of the human gut microbiota across multiple familial generations – Valles-Colomer et al. Nature Microbiology. 

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping – Beresford-Jones et al. Cell Host & Microbe

Human skin & oral microbiome

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions – Kashaf et al. Nature Microbiology.

Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics – Jo et al. Science Translational Medicine

Microbiome-mediated incapacitation of interferon lambda production in the oral mucosa – Rodriguez-Hernandez et al. PNAS

Plant microbiome

Glutamic acid reshapes the plant microbiota to protect plants against pathogens – Kim et al. Microbiome. 

Water microbiome

Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy – Garber et al. mSphere

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution – Bowers et all. ISME


Fast and accurate metagenotyping of the human gut microbiome with GT-Pro – Shi et al. Nature Biotechnology

Rapid screening and identification of viral pathogens in metagenomic data – Song et al. BMC Medical Genomics. 

December 20, 2021

Today’s digest is a grab bag that includes research articles on the vaginal microbiota, the gut microbiota of dairy calves, microbial loads in medical waste, and more! I’ve also highlighted a non-microbiology article that found that pet dog owners were significantly less depressed than non-pet owners during the pandemic. So if you’re looking for more reasons to adopt a new furry friend, you can add this one to the list!

General microbiome

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei – Zulkefli et al. – PLOS One

Human vaginal microbiome

Vaginal microbiota of American Indian women and associations with measures of psychosocial stress – Borgogna et al. – PLOS One

Human gut microbiome

Gut microbiota features associated with Clostridioides difficile colonization in dairy calves – Redding et al. – PLOS One

Animal microbiome

Culicoides Latreille (Diptera: Ceratopogonidae) as potential vectors for Leishmania martiniquensis and Trypanosoma sp. in northern Thailand – Sunantaraporn et al. – PLOS Neglected Tropical Diseases

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China – Yuan et al. – PLOS One

Plant, root, and soil microbiome

Characterization of soils conducive and non-conducive to Prunus replant disease – Khan et al. – Plos One

Built environment

Disposal habits and microbial load of solid medical waste in sub-district healthcare facilities and households in Yilo-Krobo municipality, Ghana – Egbenyah et al. – PLOS One

Phages and viruses

A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus – Celone et al. – PLOS Neglected Tropical Diseases


Genomic prediction using low-coverage portable Nanopore sequencing – Lamb et al. – PLOS One

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations – Lim et al. – PLOS One

Kara’s non-microbiology pick

***Depression, anxiety, and happiness in dog owners and potential dog owners during the COVID-19 pandemic in the United States – Martin et al. – PLOS One

October 29, 2021

Sorry for the delayed post, WordPress was playing some mean tricks on me today and there were no treats! Good morning all and happy spooky season! It’s been a moment since I’ve written a post and I write to you now as a freshly (pepper)minted PhD! I’m feeling gourd and can’t wait to pumpkin spice things up with some fangtastic papers.

Some of the highlights include a paper by McAlpine et al. examining interkingdom relationships between bacteria and fungi. Specifically, they found that the gut commensal species Lactobacillus can produce a small molecule that blocks filamentous growth of the opportunistic pathogen Candida albicans. Another interesting paper comes from Michael Adams lab at the University of Georgia, Athens which showed that members of the gut microbiota have the capacity to assimilate the metal tungsten which, in turn, allows these microbes to oxidize a broad range of aldehydes in the gut. Additionally, a paper by Plummer et al. looked at the vaginal microbiota of women who have recurrent bacterial vaginosis as well as the penile microbiota of their partners, and found that when males also underwent antibiotic treatment it led to a decrease in bacterial vaginosis in their female partners.

Hope you enjoy reading these fa-boo-lous papers and may you eat, drink, and be scary this Halloween!

General Microbiome
A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase. – MacAlpine, J. et al., Nature Communications.

Pregnancy and Early-Life
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. – Laursen, M.F. et al., Nature Microbiology.

Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection. – Heiss, B.E. et al., Gut Microbes.

Mother’s Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis. – Gołębiewski. M. et al., Nutrients.

Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. – Pärnänen, K.M.M. et al., The American Journal of Clinical Nutrition.

Human Vaginal Microbiome
A Prospective, Open-Label Pilot Study of Concurrent Male Partner Treatment for Bacterial Vaginosis. – Plummer, E.L. et al., mBio.

Human Gut Microbiome
Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome. – Schut, G.J. et al., PNAS.

Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis. – Pernigoni, N. et al., Science.

Vertebrate host phylogeny influences gut archaeal diversity. – Youngblut, N.D. et al., Nature Microbiology.

Gut microbiota dysbiosis contributes to the development of chronic obstructive pulmonary disease. – Li, N. et al., Respiratory Research.

Oral Administration of Latilactobacillus sakei ADM14 Improves Lipid Metabolism and Fecal Microbiota Profile Associated With Metabolic Dysfunction in a High-Fat Diet Mouse Model. – Won, S.-M. et al., Frontiers in Microbiology.

Human Oral Microbiome
Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses. – Nemoto, T. et al., mSystems.

Animal Experiments
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. – Woo, V. et al., Cell Host & Microbe.

Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia. – Vicentini, F.A. et al., Microbiome.

Lactobacillus rhamnosus GG Derived Extracellular Vesicles Modulate Gut Microbiota and Attenuate Inflammatory in DSS-Induced Colitis Mice. – Tong, L. et al., Nutrients.

Animal Microbiome
Phage Treatment Trial to Eradicate LA-MRSA from Healthy Carrier Pigs. – Tuomala, H. et al., Viruses.

Characterization of the Eukaryotic Virome of Mice from Different Sources. – Zhang, C. et al., Microorganisms.

Supplemental L-Arginine Improves the Embryonic Intestine Development and Microbial Succession in a Chick Embryo Model. – Dai, D. et al., Frontiers in Nutrition.

Water and Extremophile Microbiome
Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. – Zrimec, J. et al., mBio.

Acrylate protects a marine bacterium from grazing by a ciliate predator. – Teng, Z.-J. et al., Nature Microbiology.

Plant, Root, and Soil Microbiome
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. – Mahdi, L.K. et al., ISME Journal.

Spatial Characterization of Microbial Communities on Multi-Species Leafy Greens Grown Simultaneously in the Vegetable Production Systems on the International Space Station. – Hummerick, M.E. et al., Life (Basel).

Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. – Jones, M.L. et al., Elife.

High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing. – Neil, K. et al., Molecular Systems Biology.

Visualizing transfer of microbial biomolecules by outer membrane vesicles in microbe-host-communication in vivo. – Bittel, M. et al., Journal of Extracellular Vesicles.

October 22, 2021

Happy Friday!

Today’s digest includes an article on the role of age in the human intestinal microbiome, research on the role of a novel Acidobacteriota in seafloor sulfur cycling, work demonstrating the use of machine learning to predict camplyobacter source data, and much more! I also included the link to a page on “The Secret World Inside You”, a science exhibit focused on the human microbiome that is at the Witte Museum in San Antonio, Texas from now until April 10, 2022. If anyone ends up checking it out, I’d love to hear about it!


A microbiome science exhibit, “The Secret World Inside You,” is at The Witte Museum in San Antonio, Texas from October 16, 2021 to April 10, 2022 .

Human gut microbiome

Bile acid-independent protection against Clostridioides difficile infection – Aguirre et al. – PLOS PATHOGENS

The importance of age in compositional and functional profiling of the human intestinal microbiome – Herzog et al. – PLOS ONE

Plant, root, and soil microbiome

The chosen few—variations in common and rare soil bacteria across biomes – Bickel & Or – The ISME Journal

The fungus Kalmusia longispora is able to cause vascular necrosis on Vitis vinifera – Karácsony et al. – PLOS ONE

Water and extremophile microbiome

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling – Flieder et al. – The ISME Journal

Beach sand oil spills select for generalist microbial populations – Heritier-Robbins et al. – The ISME Journal

Preprint: Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA – Matsuoka et al. – bioRxiv

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake – Reboul et al. – The ISME Journal

Phages and viruses

Review: Community context matters for bacteria-phage ecology and evolution – Blazanin & Turner – The ISME Journal


Machine learning to predict the source of campylobacteriosis using whole genome data – Arning et al. – PLOS GENETICS

July 2nd, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of interesting gut microbiome papers and preprints. In particular, Beller et al. looked at the succession of microbial communities in the infant gut from birth to 1 year of age. This digest also contains some very interesting works on environmental microbiome, as an example, Wasmund et al. investigated bacterial taxa able to degrade extracellular DNA in marine sediments.

For those interesting in bioinformatic tools and methods, this digest also contains the description of novel data ressources and tools. In particular, Pellow et al. present a new tool, SCAPP, allowing for a better assembly of plasmids from metagenomes.

Finally, today’s non-microbiology pick is a paper looking critically at the open source citation advantage effect (the hypothesis that articles made available open access may benefit from an increased number of citation) by conducting a meta-analysis of previous studies.

Have a great Weekend!

Multi-site human microbiome

Review: The human microbiome and COVID-19: A systematic review – Yamamoto et al. – Plos One

Human gut microbiome

The gut microbiome and type 2 diabetes status in the Multiethnic Cohort – Maskarinec et al. – Plos One

Preprint: Niche partitioning facilitates coexistence of closely related gut bacteria – Brochet et al. – BiorXiV

Preprint: Successional Stages in Infant Gut Microbiota Maturation – Beller et al. – BiorXiV

Fetal meconium does not have a detectable microbiota before birth – Kennedy et al. – Nature Microbiology

Animal experiments

Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study – Tal et al. – NPJ Biofilms and Microbiomes

Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance – Liu et al. – Nature Microbiology

Animal microbiome

Preprint: Enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic chronic diarrhea – Delwart et al. – BiorXiV

Plant, root, and soil microbiome

Microbiomes of commercially-available pine nuts and sesame seeds – Fay et al. – Plos One

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication – Van Cauwenberghe et al. – ISME Journal

Water and extremophile microbiome

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments – Wasmund et al. – Nature Microbiology

Phages and viruses

Preprint: High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems – Meaden et al. – BioRxiV

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome – Nayfach et al. – Nature Microbiology


SCAPP: an algorithm for improved plasmid assembly in metagenomes – Pellow et al. – Microbiome

A standardized archaeal taxonomy for the Genome Taxonomy Database – Rinke et al. – Nature Microbiology

My non-microbiology picks

Is the open access citation advantage real? A systematic review of the citation of open access and subscription-based articles – Langham-Putrow et al. – Plos One

June 23, 2021

Happy Wednesday!

Today’s digest includes a review on the microbial transformations of human bile acids as well as research articles focused on extremophiles including Arthrobacter, Acidithiobacillus, and Atribacteria. Also included are a wide variety of preprints on topics such as CRISPR-Cas, the vaginal microbiome, immunocompetence in pigs, the evaluation of RNAlater for preserving field samples for metaproteomics, and more!

Happy reading!

General microbiome

Preprint: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids – Pinilla-Redondo et al. – bioRxiv

Human respiratory microbiome

Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students – Fu et al. – Microbiome

Human vaginal microbiome

Preprint: Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data – France et al. – bioRxiv

Human gut microbiome

Review: Microbial transformations of human bile acids – Guzior & Quinn – Microbiome

Preprint: Targeted high-resolution taxonomic identification of Bifidobacterium longum subsp. infantis using human milk oligosaccharide metabolizing genes – Tso et al. – bioRxiv

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants – Xie et al. – Microbiome

Animal experiments

Preprint: Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs – Ramayo-Caldas et al. – bioRxiv

Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens – Wen et al. – Microbiome

Animal microbiome

Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish – Röthig et al. – Microbiome

Plant, root, and soil microbiome

Preprint: Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments – Glass et al. – bioRxiv

Preprint: Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – bioRxiv

Preprint: The activity and functions of subarctic soil microbial communities vary across vegetation types – Viitamäki et al. – bioRxiv

Water and extremophile microbiome

Preprint: Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep – Chen et al. – bioRxiv

Preprint: Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures – Li et al. – bioRxiv

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir – Mo et al. – Microbiome

Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution – Shen et al. – Microbiome

Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs – Sriaporn et al. – Microbiome

Built environment

Preprint: Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking – Suttner et al. – bioRxiv

Phages and viruses

Preprint: Expanding clinical phage microbiology: Simulating phage inhalation for respiratory tract infections – Porat et al. – bioRxiv


Ultra-accurate microbial amplicon sequencing with synthetic long reads – Callahan et al. – Microbiome

Preprint: Evaluation of RNAlater as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses – Jensen et al. – bioRxiv

Preprint: Predicting microbiome compositions through deep learning – Michel-Mata et al. – bioRxiv

June 4, 2021

Greetings from Pittsburgh!

Today’s digest includes a review about the digestibility of adult dog diets, several articles about the human gut microbiome, an article about the spinach phyllosphere, and research about the effect of fertilizer and continuous garlic cultivation on the soil microbiome. It also includes topics such as microorganisms in ancient Siberian permafrost, the use of a probiotic consortium as an alternative to chemical remediation of oil spills, and much more!

If you want a lighter read, I’ve also included a fun Smithsonian Magazine article about the use of bacteria in art restoration.

Happy Friday!

General microbiome

Review: An evolving view on biogeochemical cycling of iron – Kappler et al. – Nature Reviews Microbiology

Review: Beyond horizontal gene transfer: the role of plasmids in bacterial evolution – Rodríguez-Beltrán et al. – Nature Reviews Microbiology

Review: Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle – Salje – Nature Reviews Microbiology

Reviews: Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions – Weisskopf et al. – Nature Reviews Microbiology

Human skin microbiome

Apple cider vinegar soaks do not alter the skin bacterial microbiome in atopic dermatitis – Luu et al. – PLOS One

Human gut microbiome

Metabolomic profiling identifies complex lipid species and amino acid analogues associated with response to weight loss interventions – Bihlmeyer et al. – PLOS One

Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus – Kitten et al. – PLOS One

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank – Liu et al. – Microbiome

Gut microbiota profiles of young South Indian children: Child sex-specific relations with growth – Shivakumar et al. – PLOS One

Animal experiments

Review: Soybean meal and poultry offal meal effects on digestibility of adult dogs diets – Vanelli et al. – PLOS One

Animal microbiome

A survey of mosquito-borne and insect-specific viruses in hospitals and livestock markets in western Kenya – Chiuya et al. – PLOS One

Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact – Émie et al. – Microbiome

Characterization of oral and cloacal microbial communities in cold-stunned Kemp’s ridley sea turtles (Lepidochelys kempii) during the time course of rehabilitation – McNally et al. – PLOS One

Plant, root, and soil microbiome

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage – Ibekwe et al. – PLOS One

Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic – Zhou et al. – PLOS One

Water and extremophile microbiome

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale – Carnevali et al. – Microbiome

Urban wastewater bacterial communities assemble into seasonal steady states – LaMartina et al. – Microbiome

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost – Liang et al. – Microbiome

Genomic and immunogenic changes of Piscine novirhabdovirus (Viral Hemorrhagic Septicemia Virus) over its evolutionary history in the Laurentian Great Lakes – Niner et al. – PLOS One

Built environment

Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites – Silva et al. – Microbiome

Microbes in the news

Italian Art Restorers Used Bacteria to Clean Michelangelo Masterpieces – Davis-Marks – Smithsonian Magazine